Hi Gregor,<div><br></div><div>I have had some more time to think about this issue.</div><div><br></div><div>In an ideal world the combination of genus and specific epithet should map to one concept.</div><div><br></div><div>
I believe that was Linnaeus's original intent.</div><div><br></div><div>Unfortunately the current system seems to have strayed from this original goal.</div><div><br></div><div>Also, it was unanticipated that changes in phylogenetic thinking would cause as many changes to the "identifier: or name for a given species.</div>
<div><br></div><div>Dima and I came up with the somewhat strange URI's for name strings so we could look at ways to connect some sort of species concept to the various names in the GNI.</div><div><br></div><div>The GNI itself does not always know what kind of thing a given name string represents.</div>
<div><br></div><div>It also does not know if a given name string is valid or not.</div><div><br></div><div>The GNI needs some additional parts to make sense of these. I will leave it to others to describe those additional parts.</div>
<div><br></div><div>After looking through a large set of species related publications etc. it is clear that the vast majority of information sources only list the genus and specific epithet.</div><div><br></div><div>To make sense of those and do entity extraction etc. I think the following service would be useful.</div>
<div><br></div><div>You have a name, lets say Duplictus annoyii.</div><div><br></div><div>To get information about what that name might be you reference a semantic web service using a URL form of the name.</div><div><br></div>
<div><a href="http://example.org/names/Duplictus_annoyii">http://example.org/names/Duplictus_annoyii</a></div><div><br></div><div>If you a human using a web browser this will return a page that lists all the things it might be.</div>
<div><br></div><div>Kingdom Animalia <meta charset="utf-8">Duplictus annoyii Schmoe 1886 => appears in database in X, Y, Z</div><div><meta charset="utf-8">Kingdom Animalia Duplictus annoyii Schmoe 1886 sec Thomas 1920 => appears in database in A, I, P</div>
<meta charset="utf-8"><div>Kingdom Plantae Duplictus annoyii Carefulnot => appears in database M</div><meta charset="utf-8"><meta charset="utf-8"><div><br></div><div>If there are no exact matches it could return:</div>
<div><br></div><div>Similar Name Strings</div><div><meta charset="utf-8"><div>Kingdom Animalia Duplictus annoyi Schmoe 1886 => appears in database in X, Y, Z</div><meta charset="utf-8"></div><div><meta charset="utf-8"><div>
<div>Kingdom <meta charset="utf-8">Plantae Duplictus annous Carefulnot => appears in database in A, I, P</div><meta charset="utf-8"><div><meta charset="utf-8">Kingdom Plantae Duplictus annous Carefulnot => appears in database M</div>
<meta charset="utf-8"><meta charset="utf-8"></div></div><div><meta charset="utf-8"><div><div><div>Kingdom Plantae Duplicta annous (Carefulnot) => appears in database in X, Y, Z</div><div><br></div><div>A semantic web program would receive an RDF version of the information above and could use various heuristics to determine which are the most likely full names.</div>
<div><br></div><div>Eventually the service could also include opinions about which name variants are valid and which are not.</div><div><br></div><div><meta charset="utf-8">Felis concolor => Felis concolor Linnaeus 1771</div>
<meta charset="utf-8"><div><br></div><div>"Valid" names would include properly formed synonyms so Felis concolor would return Felis concolor Linnaeus 1771.</div><meta charset="utf-8"></div></div></div><div><br></div>
<div>The associated URLs for each of these forms would be</div><div><br></div><div><meta charset="utf-8">HTML Page <a href="http://example.org/names/Duplictus_annoyii.html">http://example.org/names/Duplictus_annoyii.html</a></div>
<div><br></div><div><meta charset="utf-8">RDF Page <a href="http://example.org/names/Duplictus_annoyii.rdf">http://example.org/names/Duplictus_annoyii.rdf</a></div><div><br></div><div>This service would help map a given genus specific epithet combination to possible full scientific names with authorship.</div>
<div><br></div><div>You would need an additional even more opinionated web service that would tell you what the most current full name is for a given scientific name with authorship.</div><div><br></div><div>One that recognizes that "Felis concolor Linnaeus 1771" is a older synonym for "Puma concolor (Linnaeus, 1771)"</div>
<div><br></div><div>In GNUB / GNITE these two URI's could be considered reconciliation groups.</div><div><br></div><div><meta charset="utf-8"><a href="http://example.org/recgroups/Animal/Felis_concolor">http://example.org/recgroups/Animal/Felis_concolor</a> => PrefName:""Felis concolor Linnaeus 1771"</div>
<meta charset="utf-8"><div><meta charset="utf-8"><a href="http://example.org/recgroups/Animal/Puma_concolor">http://example.org/recgroups/Animal/Puma_concolor</a> => PrefName:"Puma concolor (Linnaeus, 1771)"</div>
<div><br></div><div>This allows a different service or different groups to make statements about these.</div><div><br></div><div><meta charset="utf-8"><a href="http://example.org/recgroups/Animal/Felis_concolor">http://example.org/recgroups/Animal/Felis_concolor</a> olderSynonymFor <a href="http://example.org/recgroups/Animal/Puma_concolor">http://example.org/recgroups/Animal/Puma_concolor</a> </div>
<div><br></div><div>or </div><div><br></div><div><meta charset="utf-8"><a href="http://example.org/recgroups/Animal/Felis_concolor">http://example.org/recgroups/Animal/Felis_concolor</a> isBasionymOf <a href="http://example.org/recgroups/Animal/Puma_concolor">http://example.org/recgroups/Animal/Puma_concolor</a> </div>
<meta charset="utf-8"><meta charset="utf-8"><meta charset="utf-8"><meta charset="utf-8"><div><br></div><meta charset="utf-8"><div>Note that this system allows for different groups to make different an potentially conflicting statements about the different reconcillation groups.</div>
<div><br></div><div>These different statements are from different groups so can assigned to different "graphs"</div><div><br></div><div><subject> <predicate> <object> <graph></div><div><br>
</div><div>For example:</div><div><br></div><div><meta charset="utf-8"><a href="http://example.org/recgroups/Animal/Aedes_triseriatus">http://example.org/recgroups/Animal/Aedes_triseriatus</a> isPreferedNameVariantOf <speciesXYZ> <urn:<a href="http://frustrated.medical.entomologists.org">frustrated.medical.entomologists.org</a>></div>
<div><meta charset="utf-8"><a href="http://example.org/recgroups/Animal/Ochlerotatus_triseriatus">http://example.org/recgroups/Animal/Ochlerotatus_triseriatus</a> isPreferedNameVariantOf <speciesXYZ> <urn:<a href="http://frustrated.dipterist.taxonomist.org">frustrated.dipterist.taxonomist.org</a>></div>
<div><br></div><meta charset="utf-8"><div>For the vast majority of people that simply care about mapping these names to the same "thing:</div><div><br></div><div>They simply do the following in their own knowledge base.</div>
<div><br></div><div><meta charset="utf-8"><a href="http://example.org/recgroups/Animal/Aedes_triseriatus">http://example.org/recgroups/Animal/Aedes_triseriatus</a> sameAs <a href="http://example.org/recgroups/Animal/Ochlerotatus_triseriatus">http://example.org/recgroups/Animal/Ochlerotatus_triseriatus</a></div>
<div><br></div><div>Now for them facts like:</div><div><br></div><div><meta charset="utf-8"><a href="http://example.org/recgroups/Animal/Aedes_triseriatus">http://example.org/recgroups/Animal/Aedes_triseriatus</a> larvalDevelopmentIn <stdVocab:TreeHoles></div>
<div><br></div><meta charset="utf-8"><div><meta charset="utf-8"><a href="http://example.org/recgroups/Animal/Ochlerotatus_triseriatus">http://example.org/recgroups/Animal/Ochlerotatus_triseriatus</a> takesBloodMealsFrom <stdVocab:Birds></div>
<div><br></div><div><meta charset="utf-8"><a href="http://example.org/recgroups/Animal/Ochlerotatus_triseriatus">http://example.org/recgroups/Animal/Ochlerotatus_triseriatus</a> knownVectorOf <stdVocab:LacCrosseEncephalitis></div>
<div><br></div><div>Are interpreted as being statements about the same "thing"</div><div><br></div><div>Respectfully,</div><div><br></div><div>- Pete</div><meta charset="utf-8"><div><br><div class="gmail_quote">
On Thu, Nov 25, 2010 at 10:06 AM, Gregor Hagedorn <span dir="ltr"><<a href="mailto:g.m.hagedorn@gmail.com">g.m.hagedorn@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
A side remark, about where I believe the whole discussion is misleading:<br>
<div class="im"><br>
> Puma concolor se:v6n7p<br>
> That way in the future if the name changes without a change in the concept.<br>
> Eupuma concolor se:v6n7p<br>
> The data says linked.<br>
<br>
</div>This always looks nice... However, with such proposals we, the<br>
computer guys, make the concept-assessment someone elses problem (i.e.<br>
the taxonomists, ecologists, pathologist, etc.), and, at the same<br>
time, do not provide them the means to communicate. The assumption is<br>
that a scientist or applied worker would know whether to add se:v6n7p<br>
to a given taxon name or not.<br>
<br>
With my taxonomer/pathologist hat on: I mostly have no clue which<br>
concept XXX concolor is - and whether it is changed or not. Puma<br>
concolor may be a different concept than Puma concolor. We are, of<br>
course, guilty of communicating in a shamefully loose way (s.str., s.<br>
lat. etc.), which could and should be improved by citing a secundum,<br>
but beyond that: mapping concepts is a taxonomic opinion, no objective<br>
truth.<br>
<br>
So given that any trivial mapping mechanism can map multiple IDs (Puma<br>
concolor, Eupuma concolor) to a single concept - the proposal saves<br>
this trivial processing time, but does not contribute to the problem<br>
of communicating in a way that is suitable to assess taxon concepts.<br>
<br>
----<br>
<br>
Aside: Please compare the highly linked, and generally correctly<br>
linked Wikipedias with other content management system for the<br>
advantage of human legible IDs [[Puma concolor]] over<br>
<a href="http://x.y.net/node/234872561" target="_blank">http://x.y.net/node/234872561</a> - links. My own observation is that in<br>
the latter case only a fraction of the desirable links are created,<br>
and that these are quite often going to wrong, or perhaps obsoleted<br>
places.<br>
<br>
I therefore think:<br>
se:Puma_concolor_sec._Smith<br>
would be a much more useful mechanism than all the<br>
computer-scientists-only proposals like se:v6n7p or<br>
<div><div></div><div class="h5"><a href="http://gni.globalnames.org/name_strings/772d5162-f5aa-596c-98e0-a1c6c5a29bb9" target="_blank">http://gni.globalnames.org/name_strings/772d5162-f5aa-596c-98e0-a1c6c5a29bb9</a><br>
<br>
</div></div><font color="#888888">Gregor<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>---------------------------------------------------------------<br>Pete DeVries<br>Department of Entomology<br>University of Wisconsin - Madison<br>445 Russell Laboratories<br>
1630 Linden Drive<br>Madison, WI 53706<br><a href="http://www.taxonconcept.org/" target="_blank">TaxonConcept Knowledge Base</a> / <a href="http://lod.geospecies.org/" target="_blank">GeoSpecies Knowledge Base</a><br><a href="http://about.geospecies.org/" target="_blank">About the GeoSpecies Knowledge Base</a><br>
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